Table 2. Results of molecular docking (PDB ID: 1AQD), DRB1 (MHC class II haplotype) with B-cell epitopes showing good binding.
| Epitope | CABS DOCK | Docking score HEX 8.0 version | ||
| Cluster density | Ave RMSD | Max RMSD | E-Score | |
| AGQSVVSVKLAGNSS | 114.558 | 0.881 | 10.4599 | -470.84 |
| GQSVVSVKLAGNSSL | 39.2913 | 1.80702 | 22.8967 | -470.84 |
| KTSVTLAGNSSLCSI | 72.113 | 1.38671 | 2.74745 | -464.24 |
| DKTSVTLAGNSSLCS | 37.122 | 3.04378 | 21.374 | -504.26 |
| SDILLKFSPTEITAP | 40.0217 | 5.14721 | 35.8884 | -509.75 |
| DILLKFSPTEITAPT | 35.676 | 3.72797 | 11.7607 | -521.78 |
| CABS: Carbon Alpha (Cα), carbon Beta and the Side-chain Dock. The three pseudo-atoms represent each amino acid residue. E value: Energy of docking. The HEX program carries out a complete search over all six rigid-body degrees of freedom by rotating and translating the expansion coefficients. RMSD: Root Mean Square Deviation. | ||||